High contiguity de novo genome assembly and DNA modification analyses for the fungus fly, Sciara coprophila, using single-molecule sequencing
Abstract Background The lower Dipteran fungus fly, Sciara coprophila, has many unique biological features that challenge the rule of genome DNA constancy. For example, Sciara undergoes paternal chromosome elimination and maternal X chromosome nondisjunction during spermatogenesis, paternal X elimina...
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doaj-dc3a54e02e7144beacef28bd220d2a9e2021-09-12T11:28:02ZengBMCBMC Genomics1471-21642021-09-0122112310.1186/s12864-021-07926-2High contiguity de novo genome assembly and DNA modification analyses for the fungus fly, Sciara coprophila, using single-molecule sequencingJohn M. Urban0Michael S. Foulk1Jacob E. Bliss2C. Michelle Coleman3Nanyan Lu4Reza Mazloom5Susan J. Brown6Allan C. Spradling7Susan A. Gerbi8Department of Molecular Biology, Cell Biology and Biochemistry, Brown University Division of Biology and Medicine, Sidney Frank Hall for Life SciencesDepartment of Molecular Biology, Cell Biology and Biochemistry, Brown University Division of Biology and Medicine, Sidney Frank Hall for Life SciencesDepartment of Molecular Biology, Cell Biology and Biochemistry, Brown University Division of Biology and Medicine, Sidney Frank Hall for Life SciencesKSU Bioinformatics Center, Kansas State University Division of BiologyKSU Bioinformatics Center, Kansas State University Division of BiologyKSU Bioinformatics Center, Kansas State University Division of BiologyKSU Bioinformatics Center, Kansas State University Division of BiologyDepartment of Embryology, Carnegie Institution for Science, Howard Hughes Medical Institute Research LaboratoriesDepartment of Molecular Biology, Cell Biology and Biochemistry, Brown University Division of Biology and Medicine, Sidney Frank Hall for Life SciencesAbstract Background The lower Dipteran fungus fly, Sciara coprophila, has many unique biological features that challenge the rule of genome DNA constancy. For example, Sciara undergoes paternal chromosome elimination and maternal X chromosome nondisjunction during spermatogenesis, paternal X elimination during embryogenesis, intrachromosomal DNA amplification of DNA puff loci during larval development, and germline-limited chromosome elimination from all somatic cells. Paternal chromosome elimination in Sciara was the first observation of imprinting, though the mechanism remains a mystery. Here, we present the first draft genome sequence for Sciara coprophila to take a large step forward in addressing these features. Results We assembled the Sciara genome using PacBio, Nanopore, and Illumina sequencing. To find an optimal assembly using these datasets, we generated 44 short-read and 50 long-read assemblies. We ranked assemblies using 27 metrics assessing contiguity, gene content, and dataset concordance. The highest-ranking assemblies were scaffolded using BioNano optical maps. RNA-seq datasets from multiple life stages and both sexes facilitated genome annotation. A set of 66 metrics was used to select the first draft assembly for Sciara. Nearly half of the Sciara genome sequence was anchored into chromosomes, and all scaffolds were classified as X-linked or autosomal by coverage. Conclusions We determined that X-linked genes in Sciara males undergo dosage compensation. An entire bacterial genome from the Rickettsia genus, a group known to be endosymbionts in insects, was co-assembled with the Sciara genome, opening the possibility that Rickettsia may function in sex determination in Sciara. Finally, the signal level of the PacBio and Nanopore data support the presence of cytosine and adenine modifications in the Sciara genome, consistent with a possible role in imprinting.https://doi.org/10.1186/s12864-021-07926-2Genome assemblySingle molecule sequencingLong readsOptical mapsDNA modificationsEmerging model organism |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
John M. Urban Michael S. Foulk Jacob E. Bliss C. Michelle Coleman Nanyan Lu Reza Mazloom Susan J. Brown Allan C. Spradling Susan A. Gerbi |
spellingShingle |
John M. Urban Michael S. Foulk Jacob E. Bliss C. Michelle Coleman Nanyan Lu Reza Mazloom Susan J. Brown Allan C. Spradling Susan A. Gerbi High contiguity de novo genome assembly and DNA modification analyses for the fungus fly, Sciara coprophila, using single-molecule sequencing BMC Genomics Genome assembly Single molecule sequencing Long reads Optical maps DNA modifications Emerging model organism |
author_facet |
John M. Urban Michael S. Foulk Jacob E. Bliss C. Michelle Coleman Nanyan Lu Reza Mazloom Susan J. Brown Allan C. Spradling Susan A. Gerbi |
author_sort |
John M. Urban |
title |
High contiguity de novo genome assembly and DNA modification analyses for the fungus fly, Sciara coprophila, using single-molecule sequencing |
title_short |
High contiguity de novo genome assembly and DNA modification analyses for the fungus fly, Sciara coprophila, using single-molecule sequencing |
title_full |
High contiguity de novo genome assembly and DNA modification analyses for the fungus fly, Sciara coprophila, using single-molecule sequencing |
title_fullStr |
High contiguity de novo genome assembly and DNA modification analyses for the fungus fly, Sciara coprophila, using single-molecule sequencing |
title_full_unstemmed |
High contiguity de novo genome assembly and DNA modification analyses for the fungus fly, Sciara coprophila, using single-molecule sequencing |
title_sort |
high contiguity de novo genome assembly and dna modification analyses for the fungus fly, sciara coprophila, using single-molecule sequencing |
publisher |
BMC |
series |
BMC Genomics |
issn |
1471-2164 |
publishDate |
2021-09-01 |
description |
Abstract Background The lower Dipteran fungus fly, Sciara coprophila, has many unique biological features that challenge the rule of genome DNA constancy. For example, Sciara undergoes paternal chromosome elimination and maternal X chromosome nondisjunction during spermatogenesis, paternal X elimination during embryogenesis, intrachromosomal DNA amplification of DNA puff loci during larval development, and germline-limited chromosome elimination from all somatic cells. Paternal chromosome elimination in Sciara was the first observation of imprinting, though the mechanism remains a mystery. Here, we present the first draft genome sequence for Sciara coprophila to take a large step forward in addressing these features. Results We assembled the Sciara genome using PacBio, Nanopore, and Illumina sequencing. To find an optimal assembly using these datasets, we generated 44 short-read and 50 long-read assemblies. We ranked assemblies using 27 metrics assessing contiguity, gene content, and dataset concordance. The highest-ranking assemblies were scaffolded using BioNano optical maps. RNA-seq datasets from multiple life stages and both sexes facilitated genome annotation. A set of 66 metrics was used to select the first draft assembly for Sciara. Nearly half of the Sciara genome sequence was anchored into chromosomes, and all scaffolds were classified as X-linked or autosomal by coverage. Conclusions We determined that X-linked genes in Sciara males undergo dosage compensation. An entire bacterial genome from the Rickettsia genus, a group known to be endosymbionts in insects, was co-assembled with the Sciara genome, opening the possibility that Rickettsia may function in sex determination in Sciara. Finally, the signal level of the PacBio and Nanopore data support the presence of cytosine and adenine modifications in the Sciara genome, consistent with a possible role in imprinting. |
topic |
Genome assembly Single molecule sequencing Long reads Optical maps DNA modifications Emerging model organism |
url |
https://doi.org/10.1186/s12864-021-07926-2 |
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